5 speed swap wiring

I just did a 5 speed swap and things are running nice on my 02 accord. Im a little stuck on the wiring. When i had my auto ecu in i got a flashing d4. Now with my manual ecu the car thinks its in reverse (R). I wired up the vss pulling a ground from one of the old auto plugs and power from one of the wires from the big auto plug (bottom left for vss and bottom right for reverse. Both got 12.5v while car is running) then ran the signal wire directly into the ecu. Still no speedo, my thoughts are because the car thinks its in reverse. How do i change this? I connected wires 1 and 3 from the big auto harness to get it to start. Also, i wired in the reverse lights, they arent working, but when i put it in reverse the neutral light turns on in addition to the reverse light being on (on the dash). Anyone out there have any ideas what i missed or have crossed? Thanks!

Update - I've been driving a bit and no cel yet. Makes me feel like vss is good, just have to get my dash to say I'm in neutral rather than reverse. I think...

This is the DIY guide subforum. You'd likely get more help if you posted this in the appropriate subforum.

why don't you just simply unplug the light from the back of the cluster so you don't get bothered with seeing that section.